YUZA - BACSU - GREMLIN Contacts

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YUZA - Uncharacterized membrane protein YuzA

UniProt:	O32087	Sequences: MSTIQRICLVLTIIGAINWGLIGFFQFDLVAAIFGGQGSALSRIIYGLVGIAGLINLGLLFKPNEERSREEAANPEMR	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	78 (64)
Sequences:	543 (383)
Seq/√Len:	47.8

GREMLIN Results:

Legend: The darker and larger the blue dots, the higher coevolution strength.

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
16_A	53_G	5.247	1.00
24_F	47_G	3.310	1.00
28_D	31_A	3.158	1.00
3_T	7_I	2.948	1.00
10_V	60_L	2.622	1.00
21_L	29_L	2.230	1.00
12_T	56_N	2.212	1.00
31_A	46_Y	2.069	1.00
12_T	16_A	2.030	1.00
48_L	52_A	1.916	0.99
23_G	47_G	1.680	0.98
27_F	32_A	1.643	0.98
5_Q	55_I	1.557	0.97
6_R	63_P	1.543	0.97
58_G	62_K	1.466	0.96
8_C	56_N	1.427	0.95
5_Q	62_K	1.341	0.93
12_T	53_G	1.315	0.92
2_S	6_R	1.314	0.92
56_N	59_L	1.305	0.92
31_A	37_Q	1.183	0.87
17_I	54_L	1.130	0.85
52_A	56_N	1.127	0.85
6_R	61_F	1.120	0.84
50_G	54_L	1.097	0.83
40_A	44_I	1.084	0.82
30_V	45_I	1.062	0.81
20_G	27_F	1.017	0.78
11_L	52_A	0.988	0.76
28_D	37_Q	0.956	0.73
51_I	55_I	0.955	0.73
9_L	60_L	0.943	0.72
20_G	47_G	0.933	0.72
21_L	27_F	0.924	0.71
22_I	49_V	0.870	0.66
29_L	46_Y	0.859	0.65
34_F	42_S	0.844	0.64
63_P	66_E	0.774	0.57
18_N	21_L	0.774	0.57
6_R	60_L	0.773	0.57
2_S	5_Q	0.752	0.55
34_F	45_I	0.751	0.55
3_T	55_I	0.749	0.55
11_L	48_L	0.747	0.54
26_Q	38_G	0.747	0.54
35_G	49_V	0.746	0.54
14_I	62_K	0.740	0.54
28_D	42_S	0.719	0.52
8_C	59_L	0.717	0.51
12_T	22_I	0.716	0.51
7_I	55_I	0.713	0.51
33_I	45_I	0.708	0.51
9_L	59_L	0.698	0.50
12_T	20_G	0.698	0.50
51_I	66_E	0.692	0.49
39_S	42_S	0.683	0.48
55_I	58_G	0.674	0.47
20_G	24_F	0.659	0.46
13_I	30_V	0.654	0.45
6_R	57_L	0.652	0.45
5_Q	58_G	0.643	0.44
17_I	49_V	0.642	0.44
17_I	21_L	0.639	0.44
5_Q	38_G	0.637	0.43
32_A	38_G	0.633	0.43
10_V	64_N	0.619	0.42
21_L	33_I	0.602	0.40
28_D	46_Y	0.601	0.40
33_I	65_E	0.600	0.40
48_L	66_E	0.599	0.40
20_G	50_G	0.592	0.39
11_L	41_L	0.591	0.39
41_L	52_A	0.573	0.37
7_I	54_L	0.570	0.37
5_Q	61_F	0.565	0.37
43_R	47_G	0.562	0.36
26_Q	43_R	0.561	0.36
16_A	56_N	0.556	0.36
6_R	17_I	0.542	0.34
5_Q	59_L	0.539	0.34
44_I	51_I	0.531	0.33
26_Q	57_L	0.525	0.33
41_L	60_L	0.522	0.33
25_F	59_L	0.516	0.32
17_I	23_G	0.513	0.32
57_L	61_F	0.513	0.32
38_G	60_L	0.512	0.32
44_I	47_G	0.512	0.32
62_K	65_E	0.508	0.31
6_R	10_V	0.505	0.31
13_I	25_F	0.505	0.31
14_I	63_P	0.504	0.31
45_I	48_L	0.503	0.31
32_A	41_L	0.502	0.31
45_I	54_L	0.502	0.31
49_V	53_G	0.500	0.31

Legend: The i and j are positions as given in the UniProt sequence. Only predictions with Prob ≥ 0.7 are listed. For all 3L/2 predictions, click on one of the links below.

Sco = ((raw_sco - min_sco)/(avg_sco - min_sco))/2 + 0.5
Prob = P(contact | Sco, seq80/√len)
seq80 = effective number of sequences, after reducing redundancy to 80% identity

Text file of predictions (all 3L/2 predictions)
Generate restraints for ROSETTA Structure Modeling
Upload PDB model overlay contacts on the model

HHsearch Results:

Legend: GREMLIN results (Prob ≥ 0.7) overlaid on top PDB hits. The grey/red filled circles underneath are pdb residue contacts (min distance < 5 Angstroms). The shade of the circles is based on the top 10 (or top 20 if e-value < 1E-20) HHsearch results which uses the overall probability and per-site alignment prob. Inter oligomeric contacts in the pdb are in shades of red.

PDB	Chains	Cov	%	HHΔ
3fymA	1	0	4.8	0.932	Contact Map
4fbzA	3	0.8205	4	0.935	Contact Map
4hyjA	2	0.7821	3.7	0.936	Contact Map
1oahA	2	0.1026	3.6	0.936	Contact Map
4knfA	3	0.8333	3.5	0.937	Contact Map
3h90A	3	0.8974	3.5	0.937	Contact Map
4qi1A	3	0.7179	3.4	0.937	Contact Map
4tllA	1	0.9231	3.4	0.937	Contact Map
1y9iA	4	0.7436	3.3	0.937	Contact Map
4uqqA	3	0.4872	3.2	0.938	Contact Map

Sequence Conservation (Image Generated using WebLogo v3)

Legend: Color is used to show Hydrophobicity (Blue: Hydrophilic, Green: Neutral and Black: Hydrophobic). Amount of gaps is represented by width.

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